[gmx-users] restarting a crashed job

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 30 05:52:58 CEST 2011

On 30/08/2011 1:14 PM, Payman Pirzadeh wrote:
> Hello,
> My simulation crashed in the middle and I used the "/--cpi 
> checkpoint.cpt  --append"/ option to continue. However, GROMACS cannot 
> continue and complains about not being able to open the corresponding 
> .trr file. I checked my folder, the trr file is there and the name is 
> the same as the *.tpr and *.cpt files. What else could have caused 
> this problem?

Some kind of filesystem-based locking mechanism sounds most likely. If a 
zombie process of the old run still has the file, you might not be able 
to open it again. Also, check the file permissions.

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